R
Riccardo Vicedomini
Researcher at University of Paris
Publications - 18
Citations - 2887
Riccardo Vicedomini is an academic researcher from University of Paris. The author has contributed to research in topics: Metagenomics & Genome. The author has an hindex of 6, co-authored 16 publications receiving 2470 citations. Previous affiliations of Riccardo Vicedomini include Pasteur Institute & University of Udine.
Papers
More filters
Journal ArticleDOI
The Norway spruce genome sequence and conifer genome evolution.
Björn Nystedt,Nathaniel R. Street,Anna Wetterbom,Andrea Zuccolo,Yao-Cheng Lin,Douglas G. Scofield,Francesco Vezzi,Nicolas Delhomme,Stefania Giacomello,Andrey Alexeyenko,Riccardo Vicedomini,Kristoffer Sahlin,Ellen Sherwood,Malin Elfstrand,Lydia Gramzow,Kristina Holmberg,Jimmie Hällman,Olivier Keech,Lisa Klasson,Maxim Koriabine,Melis Kucukoglu,Max Käller,Johannes Luthman,Fredrik Lysholm,Totte Niittylä,Åke Olson,Nemanja Rilakovic,Carol Ritland,Josep A. Rosselló,Juliana Stival Sena,Thomas Svensson,Carlos Talavera-López,Günter Theißen,Hannele Tuominen,Kevin Vanneste,Zhiqiang Wu,Bo Zhang,Philipp Zerbe,Lars Arvestad,Lars Arvestad,Rishikesh P. Bhalerao,Joerg Bohlmann,Jean Bousquet,Rosario Garcia Gil,Torgeir R. Hvidsten,Torgeir R. Hvidsten,Pieter J. de Jong,John MacKay,Michele Morgante,Kermit Ritland,Björn Sundberg,Stacey Lee Thompson,Yves Van de Peer,Björn Andersson,Ove Nilsson,Pär K. Ingvarsson,Joakim Lundeberg,Stefan Jansson +57 more
TL;DR: The draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm, is presented, revealing numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs, which opens up new genomic avenues for conifer forestry and breeding.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,T. Roderick Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Sergey Melnikov,Bruno Vieira,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +95 more
TL;DR: The Assemblathon 2 as mentioned in this paper presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,Roderick R. Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Nicolas Maillet,Sergey Melnikov,Delphine Naquin,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Bruno Vieira,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +98 more
TL;DR: The Assemblathon 2 as discussed by the authors presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.
Journal ArticleDOI
A global metagenomic map of urban microbiomes and antimicrobial resistance
David Danko,Daniela Bezdan,Evan E. Afshin,Sofia Ahsanuddin,Chandrima Bhattacharya,Daniel Butler,Kern Rei Chng,Daisy Donnellan,Jochen Hecht,Katelyn Jackson,Katerina Kuchin,Mikhail Karasikov,Mikhail Karasikov,Mikhail Karasikov,Abigail Lyons,Lauren Mak,Dmitry Meleshko,Harun Mustafa,Harun Mustafa,Harun Mustafa,Beth Mutai,Russell Y. Neches,Amanda Ng,Olga Nikolayeva,Tatyana Nikolayeva,Eileen Png,Krista Ryon,Jorge L. Sanchez,Heba Shaaban,Maria A. Sierra,Dominique Thomas,Ben Young,Omar O. Abudayyeh,Josue Alicea,Malay Bhattacharyya,Ran Blekhman,Eduardo Castro-Nallar,Ana M. Cañas,Aspassia D. Chatziefthimiou,Robert W. Crawford,Francesca De Filippis,Youping Deng,Christelle Desnues,Emmanuel Dias-Neto,Marius Dybwad,Eran Elhaik,Danilo Ercolini,Alina Frolova,Dennis Gankin,Jonathan S. Gootenberg,Alexandra B. Graf,David C. Green,Iman Hajirasouliha,Jaden J.A. Hastings,Mark Hernandez,Gregorio Iraola,Gregorio Iraola,Gregorio Iraola,Soojin Jang,André Kahles,André Kahles,Frank J. Kelly,Kaymisha Knights,Nikos C. Kyrpides,Paweł P. Łabaj,Paweł P. Łabaj,Patrick K. H. Lee,Marcus H. Y. Leung,Per O. Ljungdahl,Gabriella Mason-Buck,Ken McGrath,Cem Meydan,Emmanuel F. Mongodin,Milton Ozório Moraes,Niranjan Nagarajan,Marina Nieto-Caballero,Houtan Noushmehr,Manuela Oliveira,Stephan Ossowski,O. Osuolale,Orhan Özcan,David Paez-Espino,Nicolás Rascovan,Hugues Richard,Hugues Richard,Gunnar Rätsch,Gunnar Rätsch,Gunnar Rätsch,Lynn M. Schriml,Torsten Semmler,Osman U. Sezerman,Leming Shi,Tieliu Shi,Rania Siam,Le Huu Song,Haruo Suzuki,Denise Syndercombe Court,Scott Tighe,Xinzhao Tong,Klas I. Udekwu,Klas I. Udekwu,Juan A. Ugalde,Brandon Valentine,Dimitar Vassilev,Elena M. Vayndorf,Thirumalaisamy P. Velavan,Jun Wu,María Mercedes Zambrano,Jifeng Zhu,Sibo Zhu,Christopher E. Mason,Natasha Abdullah,Marcos Abraao,Ait-hamlat Adel,Muhammad Afaq,Faisal Alquaddoomi,Ireen Alam,Gabriela E. Albuquerque,Alex Alexiev,Kalyn Ali,Lucia E. Alvarado-Arnez,Sarh Aly,Jennifer Amachee,Maria João Amorim,Majelia Ampadu,Muhammad Al-Fath Amran,Nala An,Watson Andrew,Harilanto Andrianjakarivony,Michael Angelov,Verónica Antelo,Catharine Aquino,Álvaro Aranguren,Luiza Ferreira de Araújo,Hitler Francois Vasquez Arevalo,Jenny Arevalo,Carme Arnan,Lucia Elena Alvarado Arnez,Fernanda Arredondo,Matthew Arthur,Freddy Asenjo,Thomas Saw Aung,Juliette Auvinet,Nuria Aventin,Sadaf Ayaz,Silva Baburyan,Abd-Manaaf Bakere,Katrin Bakhl,Thais Fernanda Bartelli,Erdenetsetseg Batdelger,François Baudon,Kevin Becher,Carla Bello,Médine Benchouaia,Hannah Benisty,Anne-Sophie Benoiston,Joseph Benson,Diego Benítez,Juliana S Bernardes,Denis Bertrand,Silvia Beurmann,Tristan Bitard-Feildel,Lucie Bittner,Christina Black,Guillaume Blanc,Brittany Blyther,Toni Bode,Julia Boeri,Bazartseren Boldgiv,Kevin Bolzli,Alexia Bordigoni,Ciro Borrelli,Sonia Bouchard,Jean-Pierre Bouly,Alicia Boyd,Gabriela P. Branco,Alessandra Breschi,Björn Brindefalk,Christian Brion,Alan Briones,Paulina Buczansla,Catherine Burke,Aszia Burrell,Alina Butova,Irvind Buttar,Jalia Bynoe,Sven Bönigk,Kari Oline Bøifot,Hiram Caballero,Xiao Wen Cai,Dayana Calderon,Angela Cantillo,Miguel Carbajo,Alessandra Carbone,Anais Cardenas,Katerine Carrillo,Laurie Casalot,Sofia Castro,Ana Valeria B Castro,Astred Castro,Ana Valeria Castro,Simone Cawthorne,Jonathan Cedillo,Salama Chaker,Jasna Chalangal,Allison Chan,Anastasia Chasapi,Starr Chatziefthimiou,Sreya Ray Chaudhuri,Akash Keluth Chavan,Francisco Chavez,Gregory Chem,Xiaoqing Chen,Michelle B. Chen,Jenn-Wei Chen,Ariel Chernomoretz,Allaeddine Chettouh,Daisy Cheung,Diana Chicas,Shirley Chiu,Hira Choudhry,Carl Chrispin,Kianna Ciaramella,Erika Cifuentes,Jake Cohen,David A. Coil,Sylvie Collin,Colleen Conger,Romain Conte,Flavia Corsi,Cecilia N. Cossio,Ana Flávia Costa,Delisia Cuebas,Bruno D'Alessandro,Katherine E. Dahlhausen,Aaron E. Darling,Pujita Das,Lucinda B. Davenport,Laurent David,Natalie R. Davidson,Gargi Dayama,Stéphane Delmas,Chris K. Deng,Chloé Dequeker,Alexandre Desert,Monika Devi,Felipe Segato Dezem,Clara N. Dias,Timothy Donahoe,Sonia Dorado,LaShonda Dorsey,Valeriia Dotsenko,Steven Du,Alexandra Dutan,Naya Eady,Jonathan A. Eisen,Miar Elaskandrany,Lennard Epping,Juan P. Escalera-Antezana,Cassie L. Ettinger,Iqra Faiz,Luice Fan,Nadine Farhat,Emile Faure,Fazlina Fauzi,Charlie Feigin,Skye Felice,Laís Pereira Ferreira,Gabriel Figueroa,Aubin Fleiss,Denisse Flores,Jhovana L. Velasco Flores,Marcos A. S. Fonseca,Jonathan Foox,Juan Carlos Forero,Aaishah Francis,Kelly French,Pablo Fresia,Jacob Friedman,Jaime J. Fuentes,Josephine Galipon,Mathilde Garcia,Laura Garcia,Catalina García,Annie Geiger,Samuel M. Gerner,Sonia L. Ghose,Dao Phuong Giang,Matías Giménez,Donato Giovannelli,Dedan Githae,Spyridon Gkotzis,Liliana Godoy,Samantha L. Goldman,Gaston H. Gonnet,Juana Gonzalez,Andrea Gonzalez,Camila Gonzalez-Poblete,Andrew N. Gray,Tranette Gregory,Charlotte Greselle,Sophie Guasco,Juan Guerra,Nika Gurianova,Wolfgang Haehr,Sebastien Halary,Felix Hartkopf,Arya Hawkins-Zafarnia,Nur Hazlin Hazrin-Chong,Eric Helfrich,Eva Hell,Tamera Henry,Samuel Hernandez,Pilar Lopez Hernandez,David Hess-Homeier,Lauren E. Hittle,Nghiem Xuan Hoan,Aliaksei Holik,Chiaki Homma,Irene Hoxie,Michael Huber,Elizabeth Humphries,Stephanie L. Hyland,Andrea Hässig,Roland Häusler,Nathalie Hüsser,Robert A. Petit,Badamnyambuu Iderzorig,Mizuki Igarashi,Shaikh B. Iqbal,Shino Ishikawa,Sakura Ishizuka,Sharah Islam,Riham Islam,Kohei Ito,Sota Ito,Takayuki Ito,Tomislav Ivankovic,Tomoki Iwashiro,Sarah S. Jackson,JoAnn Jacobs,Marisano James,Marianne Jaubert,Marie-Laure Jerier,Esmeralda Jiminez,Ayantu Jinfessa,Ymke De Jong,Hyun Woo Joo,Guilllaume Jospin,Takema Kajita,Affifah Saadah Ahmad Kassim,Nao Kato,Amrit Kaur,Inderjit Kaur,Fernanda de Souza Gomes Kehdy,Vedbar S. Khadka,Shaira Khan,Mahshid Khavari,Michelle Ki,Gina Kim,Hyung Jun Kim,Sangwan Kim,Ryan J. King,Giuseppe KoLoMonaco,Ellen Koag,Nadezhda Kobko-Litskevitch,Maryna Korshevniuk,Michael Kozhar,Jonas Krebs,Nanami Kubota,Andrii Kuklin,Sheelta S. Kumar,Rachel Kwong,Lawrence Kwong,Ingrid Lafontaine,Juliana Lago,Tsoi Ying Lai,Elodie Laine,Manolo Laiola,Olha Lakhneko,Isha Lamba,Gerardo de Lamotte,Romain Lannes,Eleonora De Lazzari,Madeline Leahy,Hyun Jung Lee,Yunmi Lee,Lucy Lee,Vincent Lemaire,Emily Leong,Dagmara Lewandowska,Chenhao Li,Weijun Liang,Moses Lin,Priscilla Lisboa,Anna Litskevitch,Eric Minwei Liu,Tracy W. Liu,Mayra Arauco Livia,Yui Him Lo,Sonia Losim,Manon Loubens,Jennifer Q. Lu,Olexandr Lykhenko,Simona Lysakova,Salah Mahmoud,Sara Abdul Majid,Natalka Makogon,Denisse Maldonado,Krizzy Mallari,Tathiane M. Malta,Maliha Mamun,Dimitri Manoir,German Marchandon,Natalia Marciniak,Sonia Marinovic,Brunna Marques,Nicole Mathews,Yuri Matsuzaki,Vincent Matthys,Madelyn May,Elias McComb,Annabelle Meagher,Adiell Melamed,Wayne Menary,Katterinne N. Mendez,Ambar Mendez,Irène Mauricette Mendy,Irene Meng,Ajay Menon,Mark Menor,Roy Meoded,Nancy Merino,Karishma Miah,Mathilde Mignotte,Tanja Miketic,Wilson Miranda,Athena Mitsios,Ryusei Miura,Kunihiko Miyake,Maria Domenica Moccia,Natasha Mohan,Mohammed Mohsin,Karobi Moitra,Mauricio Moldes,Laura Molina,Jennifer Molinet,Orgil-Erdene Molomjamts,Eftar Moniruzzaman,Sookwon Moon,Isabelle de Oliveira Moraes,Mario Moreno,Maritza S Mosella,Josef W. Moser,Christopher Mozsary,Amanda L. Muehlbauer,Oasima Muner,Muntaha Munia,Naimah Munim,Maureen Muscat,Tatjana Mustac,Cristina Muñoz,Francesca Nadalin,Areeg Naeem,Dorottya Nagy-Szakal,Mayuko Nakagawa,Ashanti Narce,Masaki Nasu,Irene González Navarrete,Hiba Naveed,Bryan Nazario,Narasimha Rao Nedunuri,Thomas Neff,Aida Nesimi,Wan Chiew Ng,Synti Ng,Gloria Nguyen,Elsy Mankah Ngwa,Agier Nicolas,Pierre Nicolas,Abdollahi Nika,Hosna Noorzi,Avigdor Nosrati,Diana N. Nunes,Kathryn O’Brien,Niamh B. O’Hara,Gabriella Oken,Rantimi A. Olawoyin,Javier Quilez Oliete,Kiara Olmeda,Tolulope Oluwadare,Itunu A. Oluwadare,Nils Ordioni,Jenessa Orpilla,Jacqueline Orrego,Melissa Ortega,Princess Osma,Israel O. Osuolale,Oluwatosin M. Osuolale,Mitsuki Ota,Francesco Oteri,Yuya Oto,Rachid Ounit,Christos A. Ouzounis,Subhamitra Pakrashi,Rachel Paras,Coral Pardo-Esté,Youngja Park,Paulina Pastuszek,Suraj Patel,Jananan Pathmanathan,Andrea Patrignani,Manuel Perez,Ante Peros,Sabrina Persaud,Anisia Peters,Adam Phillips,Lisbeth Pineda,Melissa Pool Pizzi,Alma Plaku,Alketa Plaku,Brianna Pompa-Hogan,María Gabriela Portilla,Leonardo Posada,Max Priestman,Bharath Prithiviraj,Sambhawa Priya,Phanthira Pugdeethosal,Catherine E. Pugh,Benjamin Pulatov,Angelika Pupiec,Kyrylo Pyrshev,Tao Qing,Saher Rahiel,Savlatjon Rahmatulloev,Kannan Rajendran,Aneisa Ramcharan,Adan Ramirez-Rojas,Shahryar Rana,Prashanthi Ratnanandan,Timothy D. Read,Hubert Rehrauer,Renee Richer,Alexis Rivera,Michelle Rivera,Alessandro Robertiello,Courtney Robinson,Paula Rodríguez,Nayra Aguilar Rojas,Paul Roldán,Anyelic Rosario,Sandra Roth,Maria del Mar Vivanco Ruiz,Stephen Eduard Boja Ruiz,Kaitlan Russell,Mariia Rybak,Thais S. Sabedot,Mahfuza Sabina,Ikuto Saito,Yoshitaka Saito,Gustavo Adolfo Malca Salas,Cecilia Salazar,Kaung Myat San,Jorge Sanchez,Khaliun Sanchir,Ryan Sankar,Paulo Thiago de Souza Santos,Zulena Saravi,Kai Sasaki,Yuma Sato,Masaki Sato,Seisuke Sato,Ryo Sato,Kaisei Sato,Nowshin Sayara,Steffen Schaaf,Oli Schacher,Anna-Lena M. Schinke,Ralph Schlapbach,Christian Schori,Jason R. Schriml,Felipe Segato,Felipe Sepúlveda,Marianna S. Serpa,Paola Florez de Sessions,Juan C. Severyn,Maheen Shakil,Sarah Shalaby,Aliyah Shari,Hyenah Shim,Hikaru Shirahata,Yuh Shiwa,Ophélie Da Silva,Jordana M. Silva,Gwenola Simon,Shaleni K. Singh,Kasia Sluzek,Rebecca Smith,Eunice So,Núria Andreu Somavilla,Yuya Sonohara,Nuno Rufino de Sousa,Camila P. E. de Souza,Jason Sperry,Nicolas Sprinsky,Stefan G. Stark,Antonietta La Storia,Kiyoshi Suganuma,Hamood Suliman,Jill Sullivan,Arif Asyraf Md Supie,Chisato Suzuki,Sora Takagi,Fumie Takahara,Naoya Takahashi,Kou Takahashi,Tomoki Takeda,Isabella Kuniko T. Takenaka,Soma Tanaka,Anyi Tang,Yuk Man Tang,Emilio Tarcitano,Andrea Tassinari,Mahdi Taye,Alexis Terrero,Eunice Thambiraja,Antonin Thiébaut,Sade Thomas,Andrew Maltez Thomas,Yuto Togashi,Takumi Togashi,Anna Tomaselli,Masaru Tomita,Itsuki Tomita,Oliver Toth,Nora C. Toussaint,Jennifer M. Tran,Catalina Truong,Stefan I. Tsonev,Kazutoshi Tsuda,Takafumi Tsurumaki,Michelle Tuz,Yelyzaveta Tymoshenko,Carmen Urgiles,Mariko Usui,Sophie Vacant,Laura E. Vann,Fabienne Velter,Valeria Ventorino,Patricia Vera-Wolf,Riccardo Vicedomini,Michael A. Suarez-Villamil,Sierra Vincent,Renee Vivancos-Koopman,Andrew Wan,Cindy Wang,Tomoro Warashina,Ayuki Watanabe,Samuel Weekes,Johannes Werner,David A. Westfall,Lothar H. Wieler,Michelle D. Williams,Silver A. Wolf,Brian W. Wong,Yan Ling Wong,Tyler Wong,Rasheena Wright,Tina Wunderlin,Ryota Yamanaka,Jingcheng Yang,Hirokazu Yano,George C. Yeh,Olena Yemets,Tetiana Yeskova,Shusei Yoshikawa,Laraib Zafar,Yang Zhang,Shu Zhang,Amy Zhang,Yuanting Zheng,Stas Zubenko +681 more
TL;DR: This paper presented a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over three years, representing the first systematic, worldwide catalog of the urban microbial ecosystem.
Journal ArticleDOI
GAM-NGS: genomic assemblies merger for next generation sequencing
Riccardo Vicedomini,Francesco Vezzi,Simone Scalabrin,Lars Arvestad,Lars Arvestad,Alberto Policriti +5 more
TL;DR: GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing) is a tool able to merge two or more assemblies in order to improve contiguity and correctness and avoids global alignment between contigs, making its strategy unique among other assembly reconciliation tools.